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Automation and Semantics: The CombeChem Experience. Jeremy Frey CombeDay Feb 2005. e -Science. ‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’ John Taylor, DG of UK OST

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Automation and Semantics: The CombeChem Experience

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Automation and Semantics: The CombeChem Experience

Jeremy Frey


Feb 2005

Jeremy Frey


  • ‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’John Taylor, DG of UK OST

  • ‘[The Grid] intends to make access to computing power, scientific data repositories and experimental facilities as easy as the Web makes access to information.’ TonyBlair, 2002

  • What is the web?

J G Frey


  • Trace all the way back from publication to the original data – provenanceCombeChem

  • Who needs provenance? Bush, Blair The JIC, MI5, CIA & Hutton 2004

J G Frey

The CombeChem Project

  • The exponential world of combinatorial synthesis and high throughput analysis meets the exponentially growing power of computing

    • Automation, Semantics & the Grid”

  • End to End linking of data and information

    • In chemistry this can be a very long chain –from a lab to inside a mouse

J G Frey

The CombeChem Project

  • Collect data with regard to how it could eventually be used

    • Make sure the metadata is of high quality

    • Record properly at source

  • The Chemistry Lab

    • People & Machines working together

J G Frey


  • Chemistry (Southampton & Bristol)

    • Mike Hursthouse, Chris Frampton, Jon Essex, Jeremy Frey, Guy Orpen, Stephan Christensen, Thomas Gelbrich, Sam Peppe, Hongchen Fu, Graham Tizard, Suzanna Ward, Lefteris Danos, Jamie Robinson, Kieron Taylor

  • National Crystallography Service (NCS)

    • Simon Coles, Mark Light, Ann Bingham

  • Electronics and Computer Science (Southampton)

    • Dave De Roure, Luck Moreau, Mike Luck, Hugo Mills, Graham Smith, Simon Miles, Nicky Harding, Gareth Hughes, monica Schraefel, Terry Payne

  • It-Innovation (Southampton)

    • Mike Surridge, Ken Meacham, Steve Taylor, Daren Marvin

  • Statistics (Southampton)

    • Alan Welsh, Sue Lewis, Ralph Manson, Dave Woods

  • Rutherford Appleton Laboratory –Atlas Datastore

J G Frey

  • IBM

  • U. Indiana Crystallography


  • RSC

  • IUCr

  • CombeChem Partners

  • IT

  • Innovation

  • NCS

  • Bristol Chemistry

  • ECS

  • Chemistry

  • CCDC

  • Combi

  • Centre

  • Stats

  • GSK

  • Southampton

  • AZ

  • UKOLN Bath



J G Frey

J G Frey




Smart Labs


Access to data

CombeChem Data and Knowledge Cycle

End-to-End Management










J G Frey

  • Network Dangers?

J G Frey

You still use FORTRAN!!

Chemists and programming

  • Many Chemists think that they can program

J G Frey


Some Chemistscan

What about that! His brain still uses perl scripts

J G Frey

Much more automation in modern chemistry

“That is so cool Dave, you only need a palm pilot”

J G Frey

Make sure the computer scientists know what you

actually do

J G Frey

“No, I don’t want to play chess, I just want to reheat the lasagne”

Pub/Sub for Laboratory data using a broker and ultimately delivered over GPRS

J G Frey


J G Frey

Semantic (Pervasive) Grid


J G Frey

Security and trust for experiments and data

J G Frey

Standards – now not just at the data level but metadata level as well



Must ensure this is not a problem for applications


J G Frey

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